pysam-developers/pysam

Issues

• QUAL (record.qual) listed as `Optional[int]` but actually takes a `float`

  #1316 opened 5 days ago by awgymer
  0

• CIGAR ops names in docs don't match the ones in the code

  #1255 opened 9 days ago by notestaff
  0

• `GT` field not set when creating second instance of record.

  #1308 opened 9 days ago by awgymer
  2

• A bug seems to occur when editing contigs information of a vcf header.

  #1314 opened 12 days ago by Dentalium
  0

• Request for information on VariantRecord instantiation

  #1311 opened 19 days ago by blex-max
  2

• Several tests fail: 2 failed, 155 errors

  #1284 opened a month ago by yurivict
  2

• [BUG][Typing] `PileupColumn` not imported in `libcalignmentfile.pyi`

  #1298 opened 15 days ago by vepain
  1

• Documentation contains conflicting information about the version of htslib that has been wrapped

  #1312 opened 16 days ago by wholtz
  1

• No option to flush VariantFile.write() (or at least undocumented)

  #1299 opened 23 days ago by blex-max
  2

• query_name property of AlignedSegment class typed as Optional[str]

  #1307 opened 23 days ago by svm-zhang
  1

• Confusing behaviour of `VariantRecord.filter`

  #1309 opened a month ago by awgymer
  0

• Trouble to install Pysam through Conda

  #1305 opened 2 months ago by UCMaoCell
  3

• Trying to add tags to an insilico AlignedSegment results in error

  #1304 opened 2 months ago by blex-max
  1

• HTSlib warnings can't be suppressed?

  #1303 opened 3 months ago by ohickl
  0

• Pysam ignoring some reads?

  #1300 opened 3 months ago by rLannes
  0

• [Feature request] option to ignore soft-clipped parts in get_aligned_pairs()

  #1292 opened 5 months ago by LaraFuhrmann
  6

• Unmapped pairs with pileup

  #1302 opened 3 months ago by ngaitan55
  0

• liblzma issue

  #1301 opened 3 months ago by UniAlberta
  0

• Does not parse MM tag properly with when '.' ambiguity character is present

  #1269 opened 4 months ago by ddubocan
  2

• iterating on unnamed streams

  #1297 opened 4 months ago by cmdoret
  0

• Base modifications test failing

  #1291 opened 5 months ago by SoapGentoo
  1

• fetch gives wrong results on MD tag when read CRAM files with multiple_iterators=True

  #1290 opened 5 months ago by fanxinping
  0

• Pysam returning libcurl error 77 when accessing public S3 file?

  #1257 opened 10 months ago by daisieh
  6

• In pysam 0.22.0, AlignmentFile(REMOTE_BAM) reports SSL CA cert error with remote bam files

  #1268 opened 6 months ago by litaifang
  2

• Filter line always added to the VCF header when opening a file for writing

  #1288 opened 6 months ago by nh13
  0

• Error running `bcftools plugin`

  #1287 opened 6 months ago by awgymer
  5

• Pysam on Azure ML

  #1286 opened 6 months ago by bounaux
  0

• CIRIquant: Error

  #1285 opened 6 months ago by atul2422
  0

• ModuleNotFoundError when using pysam in conda environment

  #1282 opened 6 months ago by ayushm64
  3

• about read.get_aligned_pairs(matches_only=True, with_seq=True)

  #1283 opened 6 months ago by bioinformatica
  1

• Accessing PL field is slow when number of samples gets large

  #1280 opened 6 months ago by astaric
  0

• Segmentation fault with very simple code

  #1279 opened 6 months ago by dbolser
  4

• Feature proposal: SAM tag enum

  #1272 opened 8 months ago by msto
  1

• Prebuilt wheels do not work on FIPS-compliant systems

  #1276 opened 7 months ago by shaze
  4

• Pysam .csi index support & how to deal with large references

  #1278 opened 7 months ago by RNieuwenhuis
  0

• Can't read files on s3

  #1277 opened 7 months ago by BenjaminSargsyan
  0

• import error

  #1271 opened 8 months ago by ssv1024
  0

• How can I set the compression level of a BAM file when writing?

  #1259 opened 10 months ago by clintval
  3

• AlignmentFile from String or StringIO support

  #1266 opened 9 months ago by MauroIb
  0

• variant type determination

  #1265 opened 9 months ago by arpanda
  0

• samfile.count()

  #1264 opened 9 months ago by AzureLii
  0

• ValueError: could not create iterator for region 'himom'

  #1263 opened 9 months ago by dbolser
  1

• ImportError ; libhts.so.2: cannot open shared object file: No such file or directory

  #1262 opened 10 months ago by poddarharsh15
  0

• I want to use pysam to get the PS number in the vcf file

  #1251 opened a year ago by ZON-ZONG-MIN
  1

• set_encoding_error_handler example

  #1260 opened 10 months ago by nathanLauHKGI
  0

• Allow accessing "END" as an info field to enable parsing of inter-chr SVs

  #1258 opened 10 months ago by jrobinso
  2

• Why is the site coverage of pileup different from that observed by igv？

  #1254 opened a year ago by haogecat
  2

• pileup() in 0.22 is slower than 0.16.0.1

  #1256 opened 10 months ago by Crispy13
  0

• Fails to build with Python3.12

  #1253 opened a year ago by tillea
  2

• infer_query_length ignores soft-clipped (S) bases

  #1252 opened a year ago by Manuel-DominguezCBG
  3